Originally written April 30th, 2020
knitr::opts_chunk$set(tidy = TRUE, fig.width=10, fig.height=8)
here::here()
## [1] "/Users/CPR/Academic_2019/Male_reproductive_epigenetics"
men_w_eage <- read_csv(here::here("Data/Other", "men_w_eage.csv")) %>% mutate(uncchdid = as_character(uncchdid))
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## icsex = col_character(),
## blood.draw.date = col_date(format = "")
## )
mvals <- data.table::fread(file = here::here("Data/DNAm", "mvals_cebu_final_Xincl.csv"),
select = c("V1", men_w_eage$uncchdid, "20727_R2"))
## Warning in data.table::fread(file = here::here("Data/DNAm",
## "mvals_cebu_final_Xincl.csv"), : Column name '20727' not found in column name
## header (case sensitive), skipping.
mvals <- mvals %>% column_to_rownames("V1")
Don’t worry bout the error - since 20727 is a replicate, the name doesn’t match. I add it manually.
# Loads the function for beta2m and m2beta
source(here::here("Code/EWAS", "EWAS_functions.R"))
# Originally used to calculate 5 percent variable. But loads as names_var_probes
# below. source(here('Code/functions', 'b-val_filter_5percent.R'))
names_var_probes <- read_csv(here::here("Data/DNAm", "names_var_probes_menonly_xyincl.csv"))
## Parsed with column specification:
## cols(
## probe = col_character()
## )
source(here::here("/Code/EWAS", "t_phenotype_ewas.R"))
##
## Attaching package: 'lubridate'
## The following object is masked from 'package:here':
##
## here
## The following object is masked from 'package:base':
##
## date
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
amt_summary
| (Intercept) | amt05 | age_saliva | smoke | drink | amtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 404 | 0 | 0 | 0 | 7 | 0 | 2 | 1 | 0 | 1 | 0 |
| NotSig | 136950 | 142777 | 142777 | 142777 | 142769 | 142777 | 142769 | 142776 | 142777 | 142775 | 142777 |
| Up | 5423 | 0 | 0 | 0 | 1 | 0 | 6 | 0 | 0 | 1 | 0 |
pmt_summary
| (Intercept) | pmt05 | age_saliva | smoke | drink | pmtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 490 | 0 | 0 | 0 | 9 | 0 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134752 | 142777 | 142777 | 142777 | 142765 | 142777 | 142769 | 142777 | 142777 | 142777 | 142777 |
| Up | 7535 | 0 | 0 | 0 | 3 | 0 | 6 | 0 | 0 | 0 | 0 |
father_summary
| (Intercept) | fath05c | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 492 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134770 | 142777 | 142777 | 142777 | 142767 | 142771 | 142777 | 142777 | 142777 | 142776 |
| Up | 7515 | 0 | 0 | 0 | 2 | 4 | 0 | 0 | 0 | 1 |
hhkids_summary
| (Intercept) | hholdkids05 | smoke | drink | age_blood05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 509 | 0 | 0 | 8 | 0 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134548 | 142777 | 142777 | 142767 | 142777 | 142771 | 142777 | 142777 | 142777 | 142776 |
| Up | 7720 | 0 | 0 | 2 | 0 | 4 | 0 | 0 | 0 | 1 |
icpcfat_summary
| (Intercept) | icpcfat05 | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 466 | 0 | 0 | 0 | 9 | 1 | 0 | 0 | 1 | 0 |
| NotSig | 134218 | 142777 | 142777 | 142777 | 142766 | 142771 | 142777 | 142777 | 142776 | 142777 |
| Up | 8093 | 0 | 0 | 0 | 2 | 5 | 0 | 0 | 0 | 0 |
rgrip_summary
| (Intercept) | rightgrip_mean | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 515 | 0 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134695 | 142777 | 142777 | 142777 | 142768 | 142765 | 142777 | 142777 | 142777 | 142776 |
| Up | 7567 | 0 | 0 | 0 | 2 | 10 | 0 | 0 | 0 | 1 |
blood_t_summary
| (Intercept) | log_blood_t | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 515 | 5 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134988 | 142759 | 142777 | 142777 | 142768 | 142764 | 142777 | 142777 | 142777 | 142776 |
| Up | 7274 | 13 | 0 | 0 | 2 | 11 | 0 | 0 | 0 | 1 |
source(here::here("/Code/EWAS", "repro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
romantic_summary
| (Intercept) | romantic | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 695 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132313 | 142777 | 142777 | 142777 | 142775 | 142766 | 142777 | 142777 | 142777 | 142774 |
| Up | 9769 | 0 | 0 | 0 | 1 | 9 | 0 | 0 | 0 | 3 |
sexinter_summary
| (Intercept) | sexinter | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 657 | 0 | 0 | 0 | 13 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132553 | 142777 | 142777 | 142777 | 142760 | 142767 | 142777 | 142777 | 142777 | 142776 |
| Up | 9567 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 0 | 1 |
presrela_summary
| (Intercept) | presrela | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 695 | 0 | 0 | 0 | 8 | 2 | 1 | 0 | 0 | 0 |
| NotSig | 132267 | 142777 | 142777 | 142777 | 142765 | 142767 | 142776 | 142777 | 142777 | 142776 |
| Up | 9815 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 0 | 1 |
numbsex_summary
| (Intercept) | log(numbsex + 1) | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 645 | 0 | 0 | 0 | 15 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 133144 | 142777 | 142777 | 142777 | 142758 | 142770 | 142777 | 142777 | 142777 | 142776 |
| Up | 8988 | 0 | 0 | 0 | 4 | 6 | 0 | 0 | 0 | 1 |
new_numbpreg_summary
| (Intercept) | new_numbpreg | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 698 | 1 | 0 | 0 | 12 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132292 | 142769 | 142777 | 142777 | 142759 | 142770 | 142777 | 142777 | 142777 | 142775 |
| Up | 9787 | 7 | 0 | 0 | 6 | 5 | 0 | 0 | 0 | 2 |
source(here::here("/Code/EWAS", "anthro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: attributes are not identical across measure variables;
## they will be dropped
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
height_summary
| (Intercept) | height | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 539 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 |
| NotSig | 135449 | 142777 | 142777 | 142777 | 142763 | 142767 | 142777 | 142777 | 142777 |
| Up | 6789 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 0 |
bmi_summary
| (Intercept) | bmi | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 673 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 |
| NotSig | 132250 | 142777 | 142777 | 142777 | 142765 | 142767 | 142777 | 142777 | 142776 |
| Up | 9854 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 1 |
arm_musc_area_summary
| (Intercept) | arm_musc_area | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 687 | 0 | 0 | 0 | 11 | 2 | 0 | 0 | 0 |
| NotSig | 131906 | 142777 | 142777 | 142777 | 142762 | 142767 | 142777 | 142777 | 142776 |
| Up | 10184 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 1 |
fatfree_mass_summary
| (Intercept) | fatfree_mass | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 619 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 |
| NotSig | 132115 | 142777 | 142777 | 142777 | 142765 | 142767 | 142777 | 142777 | 142777 |
| Up | 10043 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 0 |
bfperc_summary
| (Intercept) | bfperc | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 557 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 |
| NotSig | 133101 | 142777 | 142777 | 142777 | 142765 | 142767 | 142777 | 142777 | 142777 |
| Up | 9119 | 0 | 0 | 0 | 4 | 8 | 0 | 0 | 0 |
height_acc_summary
| (Intercept) | height_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 511 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 | 1 |
| NotSig | 134471 | 142777 | 142777 | 142777 | 142766 | 142765 | 142777 | 142777 | 142777 | 142776 |
| Up | 7795 | 0 | 0 | 0 | 2 | 10 | 0 | 0 | 0 | 0 |
muscle_acc_summary
| (Intercept) | muscle_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 450 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134584 | 142777 | 142777 | 142777 | 142768 | 142765 | 142777 | 142777 | 142777 | 142777 |
| Up | 7743 | 0 | 0 | 0 | 1 | 10 | 0 | 0 | 0 | 0 |
arm_acc_summary
| (Intercept) | arm_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 472 | 0 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134016 | 142777 | 142777 | 142777 | 142769 | 142766 | 142777 | 142777 | 142777 | 142777 |
| Up | 8289 | 0 | 0 | 0 | 1 | 9 | 0 | 0 | 0 | 0 |
annotation <- read.csv(here::here("/Data/DNAm", "annotation_all.csv"), header = TRUE,
nrows = 5e+05)
names(annotation)[1] <- "probe"
blood_t_annot <- merge_annot(blood_t_toptable, annotation, pval = 0.1)
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
dnam_t <- peep_dnam_pheno(top_annotation_file = blood_t_annot, pheno_file = testost)
dnam_t %>% ggplot(., aes(x = log_blood_t, y = value, group = probe, color = probe)) +
geom_point(alpha = 0.3) + stat_smooth(geom = "line", alpha = 0.5) + stat_smooth(method = "lm",
color = "gray60", alpha = 0.2) + ggpubr::theme_pubr() + theme(legend.position = "none") +
facet_wrap(~probe)
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 18 rows containing non-finite values (stat_smooth).
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 18 rows containing non-finite values (stat_smooth).
## Warning: Removed 18 rows containing missing values (geom_point).
blood_t_annot <- merge_annot(blood_t_toptable, annotation, pval = 1) %>% mutate(new_chr = as.numeric(CHR),
sig_no = if_else(adj.P.Val < 0.1, "sig", "no"))
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
qqman::qq(blood_t_annot$P.Value, main = "Q-Q plot of EWAS p-values for blood T (logged)",
col = "blue4", cex = 1.5, las = 1)
library(calibrate) # Needed for textxy used in this function
## Warning: package 'calibrate' was built under R version 3.5.2
## Loading required package: MASS
##
## Attaching package: 'MASS'
## The following object is masked _by_ '.GlobalEnv':
##
## select
## The following object is masked from 'package:dplyr':
##
## select
# This function is based on qqman packages function - I wanted to change the
# colors of the points and insert my gene names (not probe names).
CPR_manhattan(blood_t_annot, chr = "new_chr", bp = "MAPINFO", p = "P.Value", snp = "probe",
chrlabs = c(1:22, "X", "Y"), highlight = blood_t_annot %>% filter(sig_no == "sig") %>%
pull(probe), genomewideline = -log10(1.2e-05), suggestiveline = FALSE, annotatePval = 1.207018e-05,
annotateTop = FALSE, gene = "Closest_TSS_gene_name")
numbsex_annot <- merge_annot(numbsex_toptable, annotation, pval = 0.1)
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
new_numbpreg_annot <- merge_annot(new_numbpreg_toptable, annotation, pval = 0.1)
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
dnam_numbsex <- peep_dnam_pheno(top_annotation_file = numbsex_annot, pheno_file = repro)
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
dnam_new_numbpreg <- peep_dnam_pheno(top_annotation_file = new_numbpreg_annot, pheno_file = repro)
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
# dnam_numbsex %>% ggplot(., aes(x = log(numbsex) , y = value, color = probe))+
# geom_point(alpha = 0.3)+ stat_smooth(geom = 'line', alpha = 0.5)+
# stat_smooth(method = 'lm', color = 'gray60', alpha = 0.2)+
# ggpubr::theme_pubr()+ theme(legend.position = 'none')+ facet_wrap(~probe)
dnam_new_numbpreg %>% ggplot(., aes(x = new_numbpreg, y = value, group = probe, color = probe)) +
geom_point(alpha = 0.3) + stat_smooth(geom = "line", alpha = 0.5) + stat_smooth(method = "lm",
color = "gray60", alpha = 0.2) + ggpubr::theme_pubr() + theme(legend.position = "none") +
facet_wrap(~probe)
## Don't know how to automatically pick scale for object of type haven_labelled. Defaulting to continuous.
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : radius 0.000225
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : all data on boundary of neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at -0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 0.015
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 1
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : zero-width neighborhood. make span bigger
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1
## Warning: Computation failed in `stat_smooth()`:
## NA/NaN/Inf in foreign function call (arg 5)
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 8 rows containing non-finite values (stat_smooth).
## Warning: Removed 8 rows containing missing values (geom_point).
numbsex_annot <- merge_annot(numbsex_toptable, annotation, pval = 1) %>% mutate(new_chr = as.numeric(CHR),
sig_no = if_else(adj.P.Val < 0.1, "sig", "no"))
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
qqman::qq(numbsex_annot$P.Value, main = "Q-Q plot of EWAS p-values for numbsex",
col = "blue4", cex = 1.5, las = 1)
library(calibrate) # Needed for textxy used in this function
# This function is based on qqman packages function - I wanted to change the
# colors of the points and insert my gene names (not probe names).
CPR_manhattan(numbsex_annot, chr = "new_chr", bp = "MAPINFO", p = "P.Value", snp = "probe",
chrlabs = c(1:22, "X", "Y"), highlight = numbsex_annot %>% filter(sig_no == "sig") %>%
pull(probe), genomewideline = -log10(1.2e-05), suggestiveline = FALSE, annotatePval = 1.207018e-05,
annotateTop = FALSE, gene = "Closest_TSS_gene_name")
new_numbpreg_annot <- merge_annot(new_numbpreg_toptable, annotation, pval = 1) %>%
mutate(new_chr = as.numeric(CHR), sig_no = if_else(adj.P.Val < 0.1, "sig", "no"))
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
library(calibrate) # Needed for textxy used in this function
# This function is based on qqman packages function - I wanted to change the
# colors of the points and insert my gene names (not probe names).
CPR_manhattan(new_numbpreg_annot, chr = "new_chr", bp = "MAPINFO", p = "P.Value",
snp = "probe", chrlabs = c(1:22, "X", "Y"), highlight = new_numbpreg_annot %>%
filter(sig_no == "sig") %>% pull(probe), genomewideline = -log10(5.14e-06),
suggestiveline = FALSE, annotatePval = 5.150634e-06, annotateTop = FALSE, gene = "Closest_TSS_gene_name")
names_var_probes <- read_csv(here::here("Data/DNAm", "names_var_probes_m_and_f_xyincl.csv"))
## Parsed with column specification:
## cols(
## probe = col_character()
## )
source(here::here("/Code/EWAS", "t_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
amt_summary
| (Intercept) | amt05 | age_saliva | smoke | drink | amtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 421 | 0 | 0 | 0 | 8 | 2 | 2 | 1 | 0 | 1 | 0 |
| NotSig | 136970 | 143052 | 143052 | 143052 | 143041 | 143049 | 143044 | 143051 | 143052 | 143050 | 143052 |
| Up | 5661 | 0 | 0 | 0 | 3 | 1 | 6 | 0 | 0 | 1 | 0 |
pmt_summary
| (Intercept) | pmt05 | age_saliva | smoke | drink | pmtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 501 | 0 | 0 | 0 | 9 | 0 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134931 | 143052 | 143052 | 143052 | 143038 | 143052 | 143044 | 143052 | 143052 | 143052 | 143052 |
| Up | 7620 | 0 | 0 | 0 | 5 | 0 | 6 | 0 | 0 | 0 | 0 |
father_summary
| (Intercept) | fath05c | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 509 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134918 | 143052 | 143052 | 143052 | 143040 | 143046 | 143052 | 143052 | 143052 | 143051 |
| Up | 7625 | 0 | 0 | 0 | 4 | 4 | 0 | 0 | 0 | 1 |
hhkids_summary
| (Intercept) | hholdkids05 | smoke | drink | age_blood05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 526 | 0 | 0 | 8 | 0 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134682 | 143052 | 143052 | 143040 | 143052 | 143046 | 143052 | 143052 | 143052 | 143051 |
| Up | 7844 | 0 | 0 | 4 | 0 | 4 | 0 | 0 | 0 | 1 |
icpcfat_summary
| (Intercept) | icpcfat05 | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 483 | 0 | 0 | 0 | 10 | 1 | 0 | 0 | 1 | 0 |
| NotSig | 134316 | 143050 | 143052 | 143052 | 143038 | 143046 | 143052 | 143052 | 143051 | 143052 |
| Up | 8253 | 2 | 0 | 0 | 4 | 5 | 0 | 0 | 0 | 0 |
rgrip_summary
| (Intercept) | rightgrip_mean | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 536 | 0 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134843 | 143052 | 143052 | 143052 | 143041 | 143041 | 143052 | 143052 | 143052 | 143051 |
| Up | 7673 | 0 | 0 | 0 | 4 | 9 | 0 | 0 | 0 | 1 |
blood_t_summary
| (Intercept) | log_blood_t | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 540 | 14 | 0 | 0 | 8 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 135072 | 143021 | 143052 | 143052 | 143040 | 143044 | 143052 | 143052 | 143052 | 143051 |
| Up | 7440 | 17 | 0 | 0 | 4 | 6 | 0 | 0 | 0 | 1 |
source(here::here("/Code/EWAS", "repro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
romantic_summary
| (Intercept) | romantic | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 708 | 0 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132481 | 143052 | 143052 | 143052 | 143042 | 143041 | 143052 | 143052 | 143052 | 143049 |
| Up | 9863 | 0 | 0 | 0 | 3 | 9 | 0 | 0 | 0 | 3 |
sexinter_summary
| (Intercept) | sexinter | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 671 | 0 | 0 | 0 | 17 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132732 | 143052 | 143052 | 143052 | 143029 | 143042 | 143052 | 143052 | 143052 | 143051 |
| Up | 9649 | 0 | 0 | 0 | 6 | 8 | 0 | 0 | 0 | 1 |
presrela_summary
| (Intercept) | presrela | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 712 | 0 | 0 | 0 | 8 | 2 | 1 | 0 | 0 | 0 |
| NotSig | 132407 | 143052 | 143052 | 143052 | 143039 | 143042 | 143051 | 143052 | 143052 | 143051 |
| Up | 9933 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 0 | 1 |
numbsex_summary
| (Intercept) | log(numbsex + 1) | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 678 | 0 | 0 | 0 | 14 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 133216 | 143052 | 143052 | 143052 | 143033 | 143045 | 143052 | 143052 | 143052 | 143051 |
| Up | 9158 | 0 | 0 | 0 | 5 | 6 | 0 | 0 | 0 | 1 |
new_numbpreg_summary
| (Intercept) | new_numbpreg | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 704 | 1 | 0 | 0 | 12 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 132454 | 143044 | 143052 | 143052 | 143033 | 143045 | 143052 | 143052 | 143052 | 143050 |
| Up | 9894 | 7 | 0 | 0 | 7 | 5 | 0 | 0 | 0 | 2 |
source(here::here("/Code/EWAS", "anthro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: attributes are not identical across measure variables;
## they will be dropped
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
height_summary
| (Intercept) | height | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 550 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 |
| NotSig | 135524 | 143052 | 143052 | 143052 | 143037 | 143042 | 143052 | 143052 | 143052 |
| Up | 6978 | 0 | 0 | 0 | 6 | 8 | 0 | 0 | 0 |
bmi_summary
| (Intercept) | bmi | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 696 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 |
| NotSig | 132393 | 143052 | 143052 | 143052 | 143039 | 143042 | 143052 | 143052 | 143051 |
| Up | 9963 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 1 |
arm_musc_area_summary
| (Intercept) | arm_musc_area | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 702 | 0 | 0 | 0 | 11 | 2 | 0 | 0 | 0 |
| NotSig | 132105 | 143052 | 143052 | 143052 | 143036 | 143042 | 143052 | 143052 | 143051 |
| Up | 10245 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 1 |
fatfree_mass_summary
| (Intercept) | fatfree_mass | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 637 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 |
| NotSig | 132166 | 143052 | 143052 | 143052 | 143038 | 143042 | 143052 | 143052 | 143052 |
| Up | 10249 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 0 |
bfperc_summary
| (Intercept) | bfperc | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 572 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 |
| NotSig | 133089 | 143052 | 143052 | 143052 | 143038 | 143042 | 143052 | 143052 | 143052 |
| Up | 9391 | 0 | 0 | 0 | 5 | 8 | 0 | 0 | 0 |
height_acc_summary
| (Intercept) | height_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 523 | 0 | 0 | 0 | 9 | 2 | 0 | 0 | 0 | 1 |
| NotSig | 134481 | 143052 | 143052 | 143052 | 143040 | 143040 | 143052 | 143052 | 143052 | 143051 |
| Up | 8048 | 0 | 0 | 0 | 3 | 10 | 0 | 0 | 0 | 0 |
muscle_acc_summary
| (Intercept) | muscle_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 471 | 0 | 0 | 0 | 8 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134759 | 143052 | 143052 | 143052 | 143042 | 143040 | 143052 | 143052 | 143052 | 143052 |
| Up | 7822 | 0 | 0 | 0 | 2 | 10 | 0 | 0 | 0 | 0 |
arm_acc_summary
| (Intercept) | arm_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 491 | 0 | 0 | 0 | 7 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 134228 | 143052 | 143052 | 143052 | 143042 | 143041 | 143052 | 143052 | 143052 | 143052 |
| Up | 8333 | 0 | 0 | 0 | 3 | 9 | 0 | 0 | 0 | 0 |
sex_probes <- read_csv(here::here("Data/DNAm", "sex_probes.csv"))
## Parsed with column specification:
## cols(
## probe = col_character()
## )
names_var_probes <- sex_probes
source(here::here("/Code/EWAS", "t_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
amt_summary
| (Intercept) | amt05 | age_saliva | smoke | drink | amtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36697 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 351 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
pmt_summary
| (Intercept) | pmt05 | age_saliva | smoke | drink | pmtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36441 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 602 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
father_summary
| (Intercept) | fath05c | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 26 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36480 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 562 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
hhkids_summary
| (Intercept) | hholdkids05 | smoke | drink | age_blood05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 28 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36437 | 37068 | 37068 | 37066 | 37068 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 603 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
icpcfat_summary
| (Intercept) | icpcfat05 | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 22 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36437 | 37068 | 37067 | 37068 | 37066 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 609 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
rgrip_summary
| (Intercept) | rightgrip_mean | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36474 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 569 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
blood_t_summary
| (Intercept) | log_blood_t | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 32 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36368 | 37065 | 37068 | 37068 | 37066 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 668 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
source(here::here("/Code/EWAS", "repro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
romantic_summary
| (Intercept) | romantic | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 35 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36026 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37067 |
| Up | 1007 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
sexinter_summary
| (Intercept) | sexinter | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 35 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36090 | 37068 | 37068 | 37068 | 37065 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 943 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
presrela_summary
| (Intercept) | presrela | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 36 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36021 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37067 |
| Up | 1011 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
numbsex_summary
| (Intercept) | log(numbsex + 1) | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 32 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36207 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 829 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
new_numbpreg_summary
| (Intercept) | new_numbpreg | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 38 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36000 | 37066 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37067 |
| Up | 1030 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
source(here::here("/Code/EWAS", "anthro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: attributes are not identical across measure variables;
## they will be dropped
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
height_summary
| (Intercept) | height | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36656 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 |
| Up | 399 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
bmi_summary
| (Intercept) | bmi | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 35 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 35993 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37067 |
| Up | 1040 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
arm_musc_area_summary
| (Intercept) | arm_musc_area | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 38 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36064 | 37068 | 37068 | 37068 | 37066 | 37068 | 37068 | 37068 | 37068 |
| Up | 966 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 |
fatfree_mass_summary
| (Intercept) | fatfree_mass | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 41 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36068 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 |
| Up | 959 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
bfperc_summary
| (Intercept) | bfperc | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 39 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36125 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 |
| Up | 904 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
height_acc_summary
| (Intercept) | height_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36449 | 37067 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 592 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
muscle_acc_summary
| (Intercept) | muscle_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36431 | 37068 | 37068 | 37068 | 37067 | 37066 | 37068 | 37068 | 37068 | 37068 |
| Up | 613 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 0 |
arm_acc_summary
| (Intercept) | arm_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 36324 | 37068 | 37068 | 37068 | 37067 | 37068 | 37068 | 37068 | 37068 | 37068 |
| Up | 717 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
names_var_probes <- rownames(mvals) %>% data_frame() %>% rename(probe = ".")
## Warning: `data_frame()` is deprecated, use `tibble()`.
## This warning is displayed once per session.
source(here::here("/Code/EWAS", "t_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
amt_summary
| (Intercept) | amt05 | age_saliva | smoke | drink | amtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 47669 | 0 | 0 | 0 | 10 | 0 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 305808 | 444810 | 444810 | 444810 | 444789 | 444810 | 444799 | 444810 | 444810 | 444810 | 444810 |
| Up | 91333 | 0 | 0 | 0 | 11 | 0 | 9 | 0 | 0 | 0 | 0 |
pmt_summary
| (Intercept) | pmt05 | age_saliva | smoke | drink | pmtime05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Down | 42636 | 0 | 0 | 0 | 17 | 0 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 307362 | 444810 | 444810 | 444810 | 444778 | 444810 | 444805 | 444810 | 444810 | 444810 | 444810 |
| Up | 94812 | 0 | 0 | 0 | 15 | 0 | 4 | 0 | 0 | 0 | 0 |
father_summary
| (Intercept) | fath05c | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 44677 | 1 | 0 | 0 | 13 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 304617 | 444809 | 444810 | 444810 | 444786 | 444806 | 444810 | 444810 | 444810 | 444810 |
| Up | 95516 | 0 | 0 | 0 | 11 | 3 | 0 | 0 | 0 | 0 |
hhkids_summary
| (Intercept) | hholdkids05 | smoke | drink | age_blood05 | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 44747 | 1 | 0 | 12 | 0 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 304175 | 444809 | 444810 | 444786 | 444810 | 444806 | 444810 | 444810 | 444810 | 444810 |
| Up | 95888 | 0 | 0 | 12 | 0 | 3 | 0 | 0 | 0 | 0 |
icpcfat_summary
| (Intercept) | icpcfat05 | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 42525 | 0 | 0 | 0 | 9 | 0 | 0 | 0 | 0 | 0 |
| NotSig | 306060 | 444810 | 444810 | 444810 | 444789 | 444808 | 444810 | 444810 | 444810 | 444810 |
| Up | 96225 | 0 | 0 | 0 | 12 | 2 | 0 | 0 | 0 | 0 |
rgrip_summary
| (Intercept) | rightgrip_mean | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 44626 | 0 | 0 | 0 | 7 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 305747 | 444810 | 444810 | 444810 | 444792 | 444804 | 444810 | 444810 | 444810 | 444810 |
| Up | 94437 | 0 | 0 | 0 | 11 | 5 | 0 | 0 | 0 | 0 |
blood_t_summary
| (Intercept) | log_blood_t | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 41700 | 48 | 0 | 0 | 10 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 318457 | 444711 | 444810 | 444810 | 444788 | 444803 | 444810 | 444810 | 444810 | 444809 |
| Up | 84653 | 51 | 0 | 0 | 12 | 6 | 0 | 0 | 0 | 1 |
blood_t_annot <- merge_annot(blood_t_toptable, annotation, pval = 1) %>% mutate(new_chr = as.numeric(CHR),
sig_no = if_else(adj.P.Val < 0.1, "sig", "no"))
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
qqman::qq(blood_t_annot$P.Value, main = "Q-Q plot of EWAS p-values for blood T (logged)",
col = "blue4", cex = 1.5, las = 1)
library(calibrate) # Needed for textxy used in this function
# This function is based on qqman packages function - I wanted to change the
# colors of the points and insert my gene names (not probe names).
CPR_manhattan(blood_t_annot, chr = "new_chr", bp = "MAPINFO", p = "P.Value", snp = "probe",
chrlabs = c(1:22, "X", "Y"), highlight = blood_t_annot %>% filter(sig_no == "sig") %>%
pull(probe), genomewideline = -log10(1.2e-05), suggestiveline = FALSE, annotatePval = 1.207018e-05,
annotateTop = FALSE, gene = "Closest_TSS_gene_name")
blood_t_annot <- merge_annot(blood_t_toptable, annotation, pval = 1) %>% mutate(new_chr = as.numeric(CHR),
sig_no = if_else(adj.P.Val < 0.05, "sig", "no"))
## Warning: Column `probe` joining character vector and factor, coercing into
## character vector
qqman::qq(blood_t_annot$P.Value, main = "Q-Q plot of EWAS p-values for blood T (logged)",
col = "blue4", cex = 1.5, las = 1)
library(calibrate) # Needed for textxy used in this function
# This function is based on qqman packages function - I wanted to change the
# colors of the points and insert my gene names (not probe names).
CPR_manhattan(blood_t_annot, chr = "new_chr", bp = "MAPINFO", p = "P.Value", snp = "probe",
chrlabs = c(1:22, "X", "Y"), highlight = blood_t_annot %>% filter(sig_no == "sig") %>%
pull(probe), genomewideline = -log10(1.2e-05), suggestiveline = FALSE, annotatePval = 1.207018e-05,
annotateTop = FALSE, gene = "Closest_TSS_gene_name")
## Reproductive Effort EWAS
source(here::here("/Code/EWAS", "repro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
romantic_summary
| (Intercept) | romantic | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 53502 | 0 | 1 | 0 | 10 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 279513 | 444810 | 444809 | 444810 | 444789 | 444802 | 444810 | 444810 | 444810 | 444809 |
| Up | 111795 | 0 | 0 | 0 | 11 | 7 | 0 | 0 | 0 | 1 |
sexinter_summary
| (Intercept) | sexinter | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 52409 | 0 | 1 | 0 | 23 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 281515 | 444810 | 444809 | 444810 | 444771 | 444801 | 444810 | 444810 | 444810 | 444810 |
| Up | 110886 | 0 | 0 | 0 | 16 | 7 | 0 | 0 | 0 | 0 |
presrela_summary
| (Intercept) | presrela | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 53815 | 0 | 1 | 0 | 12 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 278505 | 444810 | 444809 | 444810 | 444785 | 444803 | 444810 | 444810 | 444810 | 444810 |
| Up | 112490 | 0 | 0 | 0 | 13 | 5 | 0 | 0 | 0 | 0 |
numbsex_summary
| (Intercept) | log(numbsex + 1) | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 53341 | 0 | 1 | 0 | 29 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 282281 | 444810 | 444809 | 444810 | 444765 | 444804 | 444810 | 444810 | 444810 | 444810 |
| Up | 109188 | 0 | 0 | 0 | 16 | 5 | 0 | 0 | 0 | 0 |
new_numbpreg_summary
| (Intercept) | new_numbpreg | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | bmi | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 53964 | 1 | 1 | 0 | 8 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 278493 | 444803 | 444809 | 444810 | 444789 | 444805 | 444810 | 444810 | 444810 | 444809 |
| Up | 112353 | 6 | 0 | 0 | 13 | 4 | 0 | 0 | 0 | 1 |
source(here::here("/Code/EWAS", "anthro_phenotype_ewas.R"))
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Parsed with column specification:
## cols(
## uncchdid_w_DNAm = col_character()
## )
## Warning: Missing column names filled in: 'X1' [1]
## Parsed with column specification:
## cols(
## X1 = col_double(),
## uncchdid = col_double(),
## icsex = col_character(),
## dayblood = col_double(),
## monthblood = col_double(),
## yearblood = col_double(),
## blood.draw.date = col_date(format = "")
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
## Warning: attributes are not identical across measure variables;
## they will be dropped
## Parsed with column specification:
## cols(
## uncchdid = col_double(),
## basebrgy = col_double(),
## basewman = col_double(),
## ic_dob = col_date(format = ""),
## smoke = col_double(),
## drink = col_double(),
## age_blood05 = col_double(),
## icpc1 = col_double(),
## icpc2 = col_double(),
## icpc3 = col_double(),
## icpc4 = col_double(),
## icpc5 = col_double(),
## icpc6 = col_double(),
## icpc7 = col_double(),
## icpc8 = col_double(),
## icpc9 = col_double(),
## icpc10 = col_double(),
## bmi = col_double(),
## SEAsum_83_05 = col_double()
## )
## Warning: Column `uncchdid` has different attributes on LHS and RHS of join
height_summary
| (Intercept) | height | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 51639 | 0 | 1 | 0 | 12 | 2 | 0 | 0 | 0 |
| NotSig | 290978 | 444810 | 444809 | 444810 | 444786 | 444802 | 444810 | 444810 | 444810 |
| Up | 102193 | 0 | 0 | 0 | 12 | 6 | 0 | 0 | 0 |
bmi_summary
| (Intercept) | bmi | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 53446 | 0 | 1 | 0 | 16 | 2 | 0 | 0 | 0 |
| NotSig | 278764 | 444810 | 444809 | 444810 | 444778 | 444802 | 444810 | 444810 | 444810 |
| Up | 112600 | 0 | 0 | 0 | 16 | 6 | 0 | 0 | 0 |
arm_musc_area_summary
| (Intercept) | arm_musc_area | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 56209 | 0 | 1 | 0 | 19 | 2 | 0 | 0 | 0 |
| NotSig | 271364 | 444810 | 444809 | 444810 | 444774 | 444802 | 444810 | 444810 | 444810 |
| Up | 117237 | 0 | 0 | 0 | 17 | 6 | 0 | 0 | 0 |
fatfree_mass_summary
| (Intercept) | fatfree_mass | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 55208 | 0 | 1 | 0 | 16 | 2 | 0 | 0 | 0 |
| NotSig | 267539 | 444810 | 444809 | 444810 | 444779 | 444802 | 444810 | 444810 | 444810 |
| Up | 122063 | 0 | 0 | 0 | 15 | 6 | 0 | 0 | 0 |
bfperc_summary
| (Intercept) | bfperc | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | |
|---|---|---|---|---|---|---|---|---|---|
| Down | 52017 | 0 | 1 | 0 | 16 | 2 | 0 | 0 | 0 |
| NotSig | 275480 | 444810 | 444809 | 444810 | 444778 | 444802 | 444810 | 444810 | 444810 |
| Up | 117313 | 0 | 0 | 0 | 16 | 6 | 0 | 0 | 0 |
height_acc_summary
| (Intercept) | height_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 55705 | 0 | 0 | 0 | 19 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 271025 | 444810 | 444810 | 444810 | 444779 | 444803 | 444810 | 444810 | 444810 | 444810 |
| Up | 118080 | 0 | 0 | 0 | 12 | 6 | 0 | 0 | 0 | 0 |
muscle_acc_summary
| (Intercept) | muscle_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 51939 | 0 | 0 | 0 | 21 | 2 | 0 | 0 | 0 | 0 |
| NotSig | 278293 | 444810 | 444810 | 444810 | 444778 | 444802 | 444810 | 444810 | 444810 | 444810 |
| Up | 114578 | 0 | 0 | 0 | 11 | 6 | 0 | 0 | 0 | 0 |
arm_acc_summary
| (Intercept) | arm_accretion | age_blood05 | smoke | drink | icpc1 | icpc2 | icpc3 | SEAsum_83_05 | time_bt_98_05 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Down | 50686 | 0 | 0 | 0 | 16 | 1 | 0 | 0 | 0 | 0 |
| NotSig | 282111 | 444810 | 444810 | 444810 | 444783 | 444803 | 444810 | 444810 | 444810 | 444810 |
| Up | 112013 | 0 | 0 | 0 | 11 | 6 | 0 | 0 | 0 | 0 |